2.1.3 Nucleotides and Nucleic Acids (Foundations in Biology) Flashcards
What are nucleotides made of?
- a pentose sugar
- a nitrogenous base
- a phosphate group
- all nucleotides contain the elements C, H, O, N and P
What are the roles of nucleotides?
- form the monomers of nucleic acids: RNA and DNA
- become phosphorylated nucleotides when they contain more than one phosphate group (e.g. ADP and ATP)
- help regulate metabolic pathways e.g. ATP, ADP, AMO
- components of some coenzymes e.g. NADP used in photosynthesis
What is the pentose sugar in a DNA nucleotide called?
- deoxyribose
What varies on each DNA nucleotide and what stays the same?
- the bases on each nucleotide may vary
- deoxyribose and the phosphate group stay the same
What are the four possible bases called?
- adenine (A)
- thymine (T)
- cytosine (C)
- guanine (G)
What type of base are adenine and guanine?
- purine base
What type of base are cytosine and thymine?
- pyrimidine base
What is the structure of a purine base?
- purine bases contain two carbon-nitrogen rings joined together
What is the structure of pyrimidine base?
- pyrimidine bases only have one carbon-nitrogen ring
- pyrimidine base is smaller than purine base
How many polynucleotide chains does a molecule of DNA contain?
- two polynucleotide chains
- each chain is made up of lots of nucleotides joined together
Where is DNA found?
- in the nuclei in all eukaryotic cells
- found in the cytoplasm of prokaryotic cells and some viruses
What is the role of DNA?
- the hereditary material
- carries coded instructions used in the development and functioning of all known living organisms
What is ADP and ATP?
- phosphorylated nucleotides
How do you phosphorylate a nucleotide?
- you add one or more phosphate groups to it
What does ADP and ATP contain?
- the base adenine
- the sugar ribose
- two phosphate groups (diphosphate)
- three phosphate groups (triphosphate)
What is the function for ATP?
- provides energy for chemical reactions in the cell
- ATP is synthesised from ADP and inorganic phosphate, using energy from an energy-releasing reaction e.g. the breakdown of glucose in respiration
- the ADP is phosphorylated to form ATP and a phosphate bond is formed
- energy is stored in the phosphate bond
- when the energy is needed by a cell, ATP is broken back down into ADP and inorganic phosphate
- energy is released from the phosphate bond and used by the cell
How do nucleotides join together to form polynucleotides?
- a condensation reaction between the phosphate group of one nucleotide and the sugar of another nucleotide
- forming a phosphodiester bond (consisting of the phosphate group and two ester bonds)
What is the chain of sugars and phosphates known as?
- the sugar-phosphate backbone
What bonds have to be break polynucleotides back into nucleotides?
- the phosphodiester bonds
What type of bonding allows two DNA polynucleotide strands to join together?
- hydrogen bonding between the bases
What is complementary base pairing?
- each base can only join with one specific other base to form the double helix
Which bases pair together and why?
- Adenine (A) with Thymine (T)
- Cytosine (C) with Guanine (G)
- a purine always pairs with a pyrimidine
How many hydrogen bonds form between A and T?
- two hydrogen bonds
How many hydrogen bonds form between C and G?
- three hydrogen bonds
How do the polynucleotide strands form a DNA double helix?
- two antiparallel (running in opposite directions) polynucleotide strands twist to form the DNA double-helix
Why is the DNA double helix shape good?
- compact
- easy to break the H bonds and sugar phosphate backbone as they have a strong and stable structure
- bases are protected in the middle
How do you purify DNA using a precipitation reaction?
- blend up your cells
- make up a solution of detergent, salt and distilled water
- add the broken-up cells into a beaker contains the detergent solution
- incubate in a water bath at 60 degrees for 15 mins
- then put the beaker in an ice bath to cool the mixture down
- then filter the mixture and transfer a sample to a clean boiling tube
- add protease enzymes to the filter mixture
- some proteins will breakdown
- slowly dribble some cold ethanol down the side of the tube, so it forms a layer on top of the mixture
- after a few mins, DNA will form a white precipitate
- remove this with a glass rod
Why does DNA need to copy itself?
- DNA copies itself before cell division
- so that each new cell has the full amount of DNA
How does DNA replication work?
- DNA helicase enzyme breaks the hydrogen bonds between the two polynucleotide DNA strands.
- the helix unzips to form two single strands
- DNA helicase enzyme breaks the hydrogen bonds between the two polynucleotide DNA strands.
- each original single strand acts as a template for a new strand
- free floating DNA nucleotides join to exposed bases on each original template by complementary base pairing (A with T, C with G)
- each original single strand acts as a template for a new strand
- the nucleotides of the new strand are joined together by the enzyme DNA polymerase
- this forms the sugar-phosphate backbone
- hydrogen bonds form between the bases on the original and new strand
- the strands twist to form a double helix
- the nucleotides of the new strand are joined together by the enzyme DNA polymerase
- each new DNA molecule contains one strand from the original DNA molecule and one new strand
What type of copying is DNA replication and why?
- semi-conservsation replication
- half of the strands in each new DNA molecule are from the original piece of DNA
Why does DNA replication need to be accurate?
- to make sure genetic information is conserved each time DNA in cell in replicated
What is a mutation?
- sometimes, a random, spontaneous mutation occurs
- this is any change to the DNA base sequence
- they can alter the sequence of amino acids in a protein and cause an abnormal protein to be produced
- this abnormal protein may function better or not work at all
What is a gene?
- a sequence of DNA nucleotides that codes for a polypeptide
What is a polypeptide?
- the sequence of amino acids in a polypeptide forms the primary structure of a protein
What makes each protein different?
- different proteins have a different number and order of amino acids
What determines the order of amino acids in a particular protein?
- the order of nucleotide bases in a gene
How many bases codes for each amino acid?
- a sequence of three bases (called a triplet) codes each amino acid in a gene
How are different amino acids made?
- different sequences of bases code for different amino acids
What is a template?
- the sequence of bases in a section of DNA is a template that’s used to make proteins during protein synthesis
Why does a section of DNA need to be copied into mRNA?
- DNA molecules are found in the nucleus of the cell, but ribosomes that make proteins are found in the cytoplasm
How many polynucleotide strands are there in RNA?
- one
- it is a single polynucleotide strand
What base does RNA contain instead of thymine and what base does it pair with?
- uracil (U)
- to always pairs with adenine during photosynthesis
What is messenger RNA (mRNA)?
- made in the nucleus
- three adjacent bases are called a codon
- it carries the genetic code from the DNA in the nucleus to the cytoplasm, where it’s used to make a protein during translation
What is transfer RNA (tRNA)?
- found in the cytoplasm
- it has an amino acid binding site at one end and a sequence of three bases at the other end called an anticodon
- it carries the amino acids that are used to make proteins to the ribosomes during translation
What is ribosomal RNA (rRNA)?
- forms the two subunits in a ribosome (along with proteins)
- the ribosome moves along the mRNA during protein synthesis
- the rRNA in the ribosome helps to catalyse the formation of peptide bonds between the amino acids
What is the genetic code?
- the genetic code is the sequence of base triplets (codons) in DNA or mRNA, which codes for specific amino acids
What are the three characteristic of the genetic code?
- the genetic code is:
- non-overlapping
- degenerate
- universal
Why is the genetic code non-overlapping?
- each base triplet is read in sequence, separate from the triplet before or after it
- base triplets don’t share their bases
Why is the genetic code degenerate?
- there are more possible combination of triplets than there are amino acids (20 amino acids but 64 possible triplets)
- this means some amino acids are coded for by more than one base triplet
What are the stop or start codons?
- some codons tell the cell when to start of stop production of the protein
- found at the beginning and end of the gene
- AUG is start codon
- UAG is stop codon
Why is the genetic code universal?
- the same specific base triplets code for the same amino acids in all living things
What is the definition of transcription?
- the first stage of protein synthesis where a mRNA molecule is made from the template strand of DNA
What is the definition of translation?
- second stage of protein synthesis
- when the amino acids are assembled into a polypeptide
Explain transcription
during transcription an mRNA copy of a gene is made in the nucleus:
- transcription starts when RNA polymerase (an enzyme) attaches to the DNA double-helix at the beginning of a gene
- the hydrogen bonds between the two DNA strands in the gene break, separating the strands and the DNA molecule uncoils at that point
- one of the strands is then used as a template to make an mRNA copy
- RNA polymerase lines up free RNA nucleotides alongside the template strand
- complementary base pairing means that the mRNA strand ends up being a complementary copy of the DNA template strand (except the base T is replaced by U in RNA)
- RNA polymerase lines up free RNA nucleotides alongside the template strand
- once the RNA nucleotides have paired up with their specific bases on the DNA strand, they’re joined together, forming an mRNA molecule
- the RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand
- the hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strand coils back into a double helix
- when the RNA polymerase reaches a stop codon, it stops making mRNA and detached from the DNA
- the mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm, where translation takes place
Explain translation
- Translation occurs at the ribosomes in the cytoplasm
- amino acids are joined together to make a polypeptide chain, following the sequence of codons carried by the mRNA
- the mRNA attaches itself to a ribosome and transfer RNA (tRNA) molecules carry amino acids to the ribosome
- a tRNA molecule, with an anticodon thats complementary to the start codon on the mRNA, attaches itself to the mRNA by complementary base pairing
- a second tRNA molecule attaches itself to the next codon on the mRNA in the same way
- ribosomal RNA (rRNA) in the ribosome catalyses the formation of a peptide bond between the two amino acids attached to the tRNA molecules
- this joins the amino acids together
- the first tRNA molecule moves away, leaving its amino acid behind - a third tRNA molecule binds to the next codon on the mRNA
- its amino acid binds to the first two and the second tRNA molecule moves away - this process continues, producing a polypeptide chain until there’s a stop codon on the mRNA molecule
- the polypeptide chain moves away from the ribosome and translation is complete
